Biology subjects

Ashida, H.

Publications and source records attributed to Ashida, H..

7 recordsLinked to original sources

bioRxiv2026

The anisotropic sensitivities of perceptual speed between expanding and contracting optic flows

Retinal optic flow provides critical visual cues for locomotion and self-navigation. Forward self-motion, such as walking or driving, typically induces an expanding radial flow pattern on the retina. Despite the predominance of expanding optic flow in everyday self-motion, several studies have reported higher perceptual sensitivity for contracting flow that arises under relatively rare conditions, such as walking backward or falling onto ones back. The underlying basis of this perceptual anisotropy remains elusive. In this study, we compared perceptual sensitivity to speed for expanding versus contracting optic flow, given that speed is a fundamental attribute of motion and that perceptual sensitivity to it provides insight into underlying visual mechanisms. We found that sensitivity in speed discrimination was comparable between expansion and contraction at low and high speeds, but was significantly higher for contraction at an intermediate speed corresponding to ecologically relevant self-motion, such as walking. This anisotropic pattern was observed for both 2D planar (Experiment 1) and simulated 3D (Experiment 2) optic flow stimuli. Together, these findings suggest that anisotropic perceptual sensitivity to expanding and contracting optic flow at ecologically typical egomotion speeds may reflect an adaptive visual mechanism that supports postural stability and balance during relatively rare backward self-motion.

animal behavior and cognition↗

bioRxiv2024

Gaze inversion effect: Sex invariance and difference in gaze direction sensitivity

Humans are adept at distinguishing individual faces, yet inversion dramatically impairs this ability. This face inversion effect is remarkably robust across observers, but evidence is mixed as to whether inversion also impairs the perception of facial parts, particularly the eye region. Some studies have shown that featural processing is preserved or even enhanced when faces are inverted, whereas others have reported clear inversion-related impairments in feature-based judgements. These mixed findings may reflect limited statistical power, unbalanced participant sex ratios, and heterogeneous task designs. To address these issues, we examined how strongly face inversion affects sensitivity to gaze direction in a well-powered, sex-balanced sample. A total of 190 participants judged whether the eyes in briefly presented upright or inverted faces were looking directly at them or not. Inversion reliably reduced sensitivity to gaze direction, yielding a medium-to-large effect size. Females showed modestly higher overall sensitivity than males (a small-to-medium effect), whereas the inversion effect was highly similar for females and males. These findings show that brief gaze judgements are not immune to inversion, even in a task that could in principle be based largely on eye-region information. They provide quantitative constraints that models of gaze perception should accommodate, including the largely sex-invariant inversion effect.

neuroscience↗

bioRxiv2024

Crystal structure of Bifidobacterium bifidum glycoside hydrolase family 110 α-galactosidase specific for blood group B antigen

To overcome incompatibility issues and increase the possibility of blood transfusion, technologies that enable efficient conversion of A- and B-type red blood cells to the universal donor O-type is desirable. Although several blood type-converting enzymes have been identified, detailed understanding about their molecular functions is limited. -Galactosidase from Bifidobacterium bifidum JCM 1254 (AgaBb), belonging to glycoside hydrolase (GH) 110 subfamily A, specifically acts on blood group B antigen. Here we present the crystal structure of AgaBb, including the catalytic GH110 domain and part of the C-terminal uncharacterized regions. Based on this structure, we deduced a possible binding mechanism of blood group B antigen to the active site. Site-directed mutagenesis confirmed that R270 and E380 recognize the fucose moiety in the B antigen. Thermal shift assay revealed that the C-terminal uncharacterized region significantly contributes to protein stability. This region is shared only among GH110 enzymes from B. bifidum and some Ruminococcus species. The elucidation of the molecular basis for the specific recognition of blood group B antigen is expected to lead to the practical application of blood group conversion enzymes in the future.

biochemistry↗

bioRxiv2021

CBL-C E3 ubiquitin ligase acts as a host defense to mediate ubiquitin-proteasomal degradation of enteropathogenic Escherichia coli Tir protein

Translocated intimin receptor (Tir) is an essential bacterial factor for enteropathogenic Escherichia coli (EPEC) to establish Tir-intimin interaction-mediated adherence to the epithelial cell and to form actin pedestal structures beneath the adherent bacteria. However, it remains unclear how the host cells eliminate Tir protein after infection. Here we show that intracellular translocated Tir is degraded via the host ubiquitin- proteasome system. We found that host CBL-C, an E3 ubiquitin-protein ligase, bound to and ubiquitinated the 454 tyrosine-phosphorylated Tir protein. Tir ubiquitination leads to proteasome-dependent degradation and attenuated EPEC colonization of the epithelial cell. Using Citrobacter rodentium, a mouse model for EPEC, we demonstrated that infection with C. rodentium mutant expressing a tyrosine- phenylalanine-substituted Tir (CBL-C resistant) showed increased bacterial loads in the colon and lethality compared with infection with C. rodentium expressing wild-type Tir. These results indicate that CBL-C is a critical host defense factor that determines the fate of cytosolic Tir and terminates bacterial colonization. Graphical Abstracts O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/434331v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@d28d7borg.highwire.dtl.DTLVardef@146b7e6org.highwire.dtl.DTLVardef@1d36d14org.highwire.dtl.DTLVardef@19e6b25_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Helicobacter small RNA regulates host adaptation and carcinogenesis

Type-1 carcinogenic Helicobacter pylori that is known to evolve during long-term infection, enters the stomach orally and causes gastric cancer using the carcinogenic protein CagA1. However, little is known about the adaptation mechanisms of H. pylori when the environment changes from the outside to the inside of the living body. Here we show that small non-coding RNA HPnc4160 is a crucial novel RNA molecule of H. pylori that negatively regulates bacterial-host adaptation and gastric cancer. H. pylori isolated from gerbils stomachs eight weeks post-infection acquired mutations in the increased number of T-repeats within the upstream region of the HPnc4160 coding region, which leads to reduced HPnc4160 expression levels that also seen in cancer patients-derived H. pylori. By comparing RNA-seq and iTRAQ analysis between wild-type and hpnc4160 deficient mutant strains, we identified eight targets of HPnc4160 including cagA and unknown factors. Mice infection experiment revealed that the hpnc4160 deficient mutant had a higher number of colonized bacteria in the mice stomach than the wild-type strain, indicating that reduced expression levels of HPnc4160 was important for bacterial host adaptation. The expression level of HPnc4160 was lower in the clinical isolates derived from gastric cancer patients compared with non-cancer-derived strains, while the mRNA expression levels of target factors were higher. Our findings highlight the first discovery that HPnc4160 is an important small RNA for bacteria to adapt to the host environment leading to gastric carcinogenesis.

microbiology↗

bioRxiv2018

Two Novel α-L-Arabinofuranosidases from Bifidobacterium longum subsp. longum belonging to Glycoside Hydrolase Family 43 Cooperatively Degrade Arabinan

Arabinose-containing poly-or oligosaccharides are suitable carbohydrate sources for Bifidobacterium longum subsp. longum, though their degradation pathways are poorly understood. In this study, we found that the gene expression levels of bllj 1852 and bllj 1853 from B. longum subsp. longum JCM 1217 were enhanced in the presence of arabinan. Both genes encode previously uncharacterized glycoside hydrolase (GH) family 43 enzymes. Subsequently, we cloned those genes and characterized the recombinant enzymes expressed in Escherichia coli. Both enzymes exhibited -L-arabinofuranosidase activity toward synthetic p-nitrophenyl glycoside, but the specificities for L-arabinofuranosyl linkages were different. BLLJ_1852 catalyzed the hydrolysis of 1,2- and 1,3-L-arabinofuranosyl linkages found in the side chains of arabinan and arabinoxylan. BLLJ_1852 released L-arabinose 100 times faster from arabinan than from arabinoxylan but did not act on arabinogalactan. BLLJ_1853 catalyzed the hydrolysis of 1,5-L-arabinofuranosyl linkages found on the arabinan backbone. BLLJ_1853 released L-arabinose from arabinan but not from arabinoxylan or arabinogalactan. Both enzyme activities were largely suppressed with EDTA treatment, suggesting that they require divalent metal ions. BLLJ_1852 was moderately activated in the presence of all divalent cations tested, whereas BLLJ_1853 activity was inhibited by Cu2+. The GH43 domains of BLLJ_1852 and BLLJ_1853 are classified into GH43 subfamilies 27 and 22, respectively, but hardly share similarity with other biochemically characterized members in the corresponding subfamilies.\n\nIMPORTANCEWe identified two novel -L-arabinofuranosidases from B. longum subsp. longum JCM 1217 that act on different linkages in arabinan. These enzymes may be required for efficient degradation and assimilation of arabinan in the probiotic bifidobacteria. The genes encoding these enzymes are located side-by-side in a gene cluster involved in metabolic pathways for plant-derived polysaccharides, which may confer adaptability in adult intestines.

biochemistry↗

bioRxiv2017

Computational neuroanatomy of human stratum proprium of interparietal sulcus

Recent advances in diffusion-weighted MRI (dMRI) and tractography have enabled identification of several long-range white matter tracts in the human brain. Yet, our understanding of shorter tracts, such as those within the parietal lobe, remains limited. Over a century ago, a tract connecting the superior and inferior parts of the parietal cortex was identified in a post-mortem study: Stratum proprium of interparietal sulcus (SPIS; Sachs, 1892). The tract has since been replicated in another fibre dissection study (Vergani et al. 2014), however, it has never been identified in the living human brain and its anatomical properties are yet to be described. We used dMRI and tractography to identify and characterise SPIS in vivo, and explored its spatial proximity to the cortical areas associated with optic-flow processing using fMRI. SPIS was identified bilaterally in all subjects, and its anatomical position and trajectory are consistent with previous post-mortem studies. Subsequent evaluation of the tractography results using linear fascicle evaluation and virtual lesion analysis yielded strong statistical evidence for SPIS. We also found that SPIS endpoints are adjacent to the optic-flow selective areas. In sum, we show that SPIS is a short-range tract connecting the superior and inferior parts of the parietal cortex, wrapping around the intraparietal sulcus, and that it may be a crucial anatomy underlying optic-flow processing. In vivo identification and characterisation of SPIS will facilitate further research on SPIS in relation to cortical functions, their development, and diseases that affect them.

neuroscience↗